GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UBN2 - gag-polypeptide of LTR copia-type
Pfam: PF14223 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0523
Length: 119
Sequences: 1286
Seq/Len: 10.81
HH_delta: 0.834 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
4_K8_D0.718144.969
46_Y76_S0.590794.088
29_K68_D0.455713.153
41_E49_R0.365472.529
42_S45_E0.286161.980
54_V69_L0.274291.898
82_D112_R0.247881.715
8_D12_K0.245471.699
73_I99_L0.24361.686
44_D107_L0.233031.612
88_I102_L0.229721.590
35_L50_L0.225571.561
84_F102_L0.218941.515
50_L73_I0.213021.474
12_K100_E0.209921.453
35_L46_Y0.208131.440
31_Q49_R0.196051.357
86_T109_E0.194231.344
50_L54_V0.192691.333
8_D11_K0.187371.296
73_I102_L0.187281.296
47_I73_I0.185911.286
83_T86_T0.183111.267
103_I107_L0.183061.267
41_E46_Y0.18071.250
88_I105_R0.174961.211
7_W11_K0.167251.157
43_V110_E0.167241.157
24_R28_L0.162521.125
10_L78_P0.161411.117
43_V79_P0.16041.110
14_Y48_S0.158451.096
81_Y84_F0.156221.081
69_L99_L0.155561.076
92_K101_E0.155031.073
2_T5_E0.150721.043
6_A89_R0.150561.042
103_I108_A0.150361.040
19_K101_E0.150121.039
84_F88_I0.151.038
32_L53_I0.146371.013
4_K11_K0.145841.009
58_R63_P0.14581.009
26_Q75_R0.145461.006
58_R69_L0.143050.990
98_T101_E0.143030.990
77_L81_Y0.142590.987
98_T103_I0.142540.986
10_L14_Y0.141840.981
5_E61_G0.141620.980
28_L31_Q0.141030.976
105_R108_A0.140280.971
26_Q71_S0.139460.965
52_E56_E0.138480.958
41_E45_E0.13810.956
28_L53_I0.138070.955
108_A112_R0.138050.955
43_V47_I0.13660.945
32_L72_K0.134890.933
33_E72_K0.133640.925
6_A75_R0.132960.920
88_I99_L0.131110.907
16_G19_K0.129760.898
85_V89_R0.129150.894
62_K68_D0.129080.893
25_V90_N0.128610.890
89_R112_R0.128330.888
70_V101_E0.127770.884
51_K55_D0.125650.869
70_V102_L0.125550.869
74_L88_I0.123780.856
9_A17_Q0.123520.855
36_K111_M0.123280.853
62_K65_S0.122870.850
86_T100_E0.122160.845
30_S79_P0.122150.845
2_T52_E0.122060.845
66_D73_I0.121470.841
89_R102_L0.121010.837
8_D35_L0.120870.836
70_V74_L0.120480.834
99_L103_I0.119980.830
50_L72_K0.1190.823
73_I105_R0.118830.822
30_S50_L0.118770.822
33_E75_R0.118530.820
30_S91_S0.118490.820
99_L110_E0.118380.819
14_Y85_V0.11790.816
9_A82_D0.117390.812
61_G64_I0.117350.812
5_E36_K0.117320.812
10_L84_F0.117220.811
57_L64_I0.117130.810
13_R17_Q0.116770.808
19_K23_A0.116570.807
108_A111_M0.116340.805
84_F90_N0.115790.801
11_K36_K0.115410.799
51_K81_Y0.115180.797
10_L25_V0.114750.794
69_L73_I0.114570.793
32_L69_L0.114430.792
9_A12_K0.114320.791
5_E45_E0.114070.789
47_I103_I0.113450.785
64_I95_P0.113270.784
70_V81_Y0.112220.776
89_R93_D0.11160.772
27_Q57_L0.111550.772
90_N105_R0.111480.771
36_K49_R0.111330.770
29_K72_K0.110070.762
55_D63_P0.109480.758
6_A9_A0.109350.757
46_Y104_S0.108960.754
6_A26_Q0.108780.753
72_K76_S0.108510.751
109_E112_R0.108490.751
27_Q31_Q0.108360.750
57_L102_L0.107490.744
31_Q34_N0.107280.742
16_G80_S0.107190.742
19_K71_S0.107040.741
68_D85_V0.106380.736
10_L86_T0.10580.732
25_V67_E0.105150.728
62_K70_V0.105070.727
33_E39_D0.105010.727
69_L110_E0.104940.726
63_P80_S0.104930.726
56_E90_N0.104860.726
5_E8_D0.104510.723
64_I68_D0.104140.721
86_T90_N0.103930.719
45_E55_D0.103380.715
5_E12_K0.103110.713
62_K67_E0.103010.713
86_T93_D0.102840.712
2_T9_A0.102360.708
33_E68_D0.102150.707
63_P69_L0.101860.705
10_L23_A0.101140.700
29_K62_K0.101110.700
40_G76_S0.100830.698
32_L60_I0.100650.696
3_A91_S0.100080.692
43_V46_Y0.099970.692
48_S95_P0.09980.691
54_V66_D0.09980.691
23_A26_Q0.099480.688
41_E72_K0.099410.688
23_A27_Q0.099390.688
74_L85_V0.099390.688
77_L85_V0.098760.683
57_L62_K0.098440.681
30_S89_R0.098420.681
86_T112_R0.098380.681
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
3tirA0.781572.10.834
1y7qA0.7899370.865
4f61I0.537832.90.868
3lhrA0.747932.10.869
3g21A0.647130.40.871
4bhxA0.756329.60.871
2fi2A0.756328.50.872
4e6sA0.747928.20.872
3rycE0.546227.10.874
1ez3A0.697523.80.877
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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